Briefings in Bioinformatics,
Journal Year:
2024,
Volume and Issue:
26(1)
Published: Nov. 22, 2024
Abstract
High-throughput
sequencing
data
lie
at
the
heart
of
modern
microbiome
research.
Effective
analysis
these
requires
careful
preprocessing,
modeling,
and
interpretation
to
detect
subtle
signals
avoid
spurious
associations.
In
this
review,
we
discuss
how
simulation
can
serve
as
a
sandbox
test
candidate
approaches,
creating
setting
that
mimics
real
while
providing
ground
truth.
This
is
particularly
valuable
for
power
analysis,
methods
benchmarking,
reliability
analysis.
We
explain
probability,
multivariate
regression
concepts
behind
simulators
different
implementations
make
trade-offs
between
generality,
faithfulness,
controllability.
Recognizing
all
only
approximate
reality,
review
evaluate
accurately
they
reflect
key
properties.
also
present
case
studies
demonstrating
value
in
differential
abundance
testing,
dimensionality
reduction,
network
integration.
Code
examples
available
an
online
tutorial
(https://go.wisc.edu/8994yz)
be
easily
adapted
new
problem
settings.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: Feb. 1, 2025
Abstract
Motivation
Taxonomic
analysis
of
environmental
microbial
communities
is
now
routinely
performed
thanks
to
advances
in
DNA
sequencing.
Determining
the
role
these
global
biogeochemical
cycles
requires
identification
their
metabolic
functions,
such
as
hydrogen
oxidation,
sulfur
reduction,
and
carbon
fixation.
These
functions
can
be
directly
inferred
from
metagenomics
data,
but
many
applications
metabarcoding
still
method
choice.
The
reconstruction
data
integration
into
coarse-grained
representations
geobiochemical
remains
a
difficult
bioinformatics
problem
today.
Results
We
developed
pipeline,
called
Tabigecy,
which
exploits
taxonomic
affiliations
predict
constituting
cycles.
In
first
step,
Tabigecy
uses
tool
EsMeCaTa
consensus
proteomes
input
affiliations.
To
optimise
this
process,
we
generated
precomputed
database
containing
information
about
2,404
taxa
UniProt.
are
searched
using
bigecyhmm,
newly
Python
package
relying
on
Hidden
Markov
Models
identify
key
enzymes
involved
function
then
projected
representation
applied
two
salt
cavern
datasets
validated
its
predictions
with
activity
hydrochemistry
measurements
samples.
results
highlight
utility
approach
investigate
impact
processes.
Journal of Clinical Investigation,
Journal Year:
2025,
Volume and Issue:
135(4)
Published: Feb. 16, 2025
Asthma
is
a
common
chronic
respiratory
disease
affecting
people
of
all
ages
globally.
The
airway
hosts
diverse
microbial
communities
increasingly
recognized
as
influential
in
the
development
and
course
asthma.
Here,
we
review
recent
findings
on
microbiome
As
relationships
between
health
take
root
early
life,
first
provide
an
overview
early-life
asthma
development,
where
multiple
cohort
studies
have
identified
bacterial
genera
infant
associated
with
risk
future
wheeze
We
then
address
current
understandings
interactions
environmental
factors,
microbiome,
asthma,
including
effects
rural/urban
environments,
pet
ownership,
smoking,
viral
illness,
antibiotics.
Next,
delve
into
what
has
been
observed
about
phenotypes
endotypes,
microbiota
control,
severity,
obesity-related
treatment
well
type
2
high,
low,
more
newly
described
multi-omic
endotypes.
discuss
emerging
approaches
to
shape
for
therapy
conclude
Review
perspectives
research
directions.
IGI Global eBooks,
Journal Year:
2025,
Volume and Issue:
unknown, P. 209 - 236
Published: March 14, 2025
Arbuscular
mycorrhizal
fungi
(AMFs)
are
behind
the
crucial
symbiosis
that
occurs
within
over
80%
of
root
systems
vascular
plants,
reputed
for
their
potentialities
regarding
plant,
soil,
and
conjecture
with
existing
microbiome.
Researchers
inclined
toward
studying
AMFs
in
occurrence
environment
currently
embracing
investigation
at
holobiont
level
sphere
natural
habitat.
Hence,
present
book
division
looks
how
metagenomics
can
provide
important
information
this
respect.
With
a
keen
interest
microbial
communities
retrieved
from
environment,
relying
on
advanced
sequencing
techniques,
investigate
composition
diversity
close-up
lens.
In
fungal
verse,
circadian
rhythm,
pioneeringly
explored
Sordariales
(Neurospora),
is
slowly
but
steadily
being
investigated
Glomerales
(Rhizoglomus),
providing
genetic
molecular
discernments
worth
spotlighting
into
bargain.
JACS Au,
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 1, 2025
As
global
pollution
continues
to
escalate,
timely
and
accurate
monitoring
is
essential
for
guiding
governance
safeguarding
public
health.
The
increasing
diversity
of
pollutants
across
environmental
matrices
poses
a
significant
challenge
instrumental
analysis
methods,
which
often
require
labor-intensive
time-consuming
sample
pretreatment.
Nanopore
technology,
an
emerging
single-molecule
technique,
presents
promising
solution
by
enabling
the
rapid
identification
multiple
targets
within
complex
mixtures
with
minimal
preparation.
A
wide
range
have
been
characterized
using
natural
biological
nanopores
or
artificial
solid-state
nanopores,
their
distinct
advantages
include
simple
preparation,
high
sensitivity,
onsite
analysis.
In
particular,
long-read
nanopore
sequencing
has
led
dramatic
improvements
in
analyses
microbial
communities,
allows
species-level
taxonomic
assignment
amplicon
sequencing,
simplifies
assembly
metagenomes.
this
Perspective,
we
review
latest
advancements
analyzing
chemical
through
sensing
techniques.
We
also
explore
challenges
that
remain
rapidly
evolving
field
provide
outlook
on
potential
transform
monitoring,
risk
assessment,
health
protection.
Microbiome,
Journal Year:
2025,
Volume and Issue:
13(1)
Published: April 8, 2025
This
editorial
piece
co-authored
by
the
Senior
Editors
at
Microbiome
aims
to
highlight
current
challenges
in
field
of
environmental
and
host-associated
microbiome
research.
We
also
take
opportunity
clarify
our
expectations
for
articles
submitted
journal.
At
Microbiome,
we
are
seeking
studies
that
provide
either
new
mechanistic
insights
into
role
microbiomes
health
systems
or
substantial
conceptual
technical
advances.
Manuscripts
need
meet
high
standards
language
accuracy,
quality
analyses,
data
protocol
availability,
including
detailed
reporting
wet-lab
silico
protocols,
all
which
can
critically
enhance
transparency
reproducibility.
think
such
efforts
essential
push
boundaries
knowledge
on
a
concerted,
international
effort.
Foods,
Journal Year:
2025,
Volume and Issue:
14(8), P. 1414 - 1414
Published: April 19, 2025
The
purpose
of
this
study
was
to
identify
the
microbial
community
raw
milk
samples
before
and
after
UV-C
irradiation
establish
fundamental
data
on
treatment
improve
safety
shelf
life
milk.
Metagenomic
analysis
revealed
that
Lactococcus
spp.,
Lactobacillus
Staphylococcus
spp.
were
dominant
genera
in
milk,
while
Pseudomonas
became
more
prevalent
14
days
refrigerated
storage.
microorganisms
isolated
using
selective
media
identified
as
Serratia
quinivorans
4364
Latilactobacillus
curvatus
DSM
20019.
To
compare
UV
resistance
these
microorganisms,
aeruginosa,
aureus,
lactis,
inoculated
into
sterilized
subjected
treatment.
reduction
rates
P.
aeruginosa
significantly
lower
than
those
other
strains
(S.
L.
curvatus).
These
findings
provide
insights
distribution
degree
treatment,
which
can
serve
for
pasteurization
